BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 026552
(237 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3P5J|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 301
Score = 187 bits (475), Expect = 4e-48, Method: Compositional matrix adjust.
Identities = 89/181 (49%), Positives = 120/181 (66%), Gaps = 3/181 (1%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 75
GWA+D++ P +S ML + K NLN +SHD+A GLI L+ + +T+V++DTVG E Y
Sbjct: 91 GWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMPETY 150
Query: 76 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 135
QA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W F E +++ ++GSG
Sbjct: 151 QARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDYGSG 210
Query: 136 YPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLWESDEMDEDVSSRRSG 194
YP DP+TKAWL H +FGFP VRFSW T + K+ +V+WE E +ED R G
Sbjct: 211 YPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIWEDSEAEED--PERPG 268
Query: 195 K 195
K
Sbjct: 269 K 269
>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex
Length = 301
Score = 185 bits (470), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 88/181 (48%), Positives = 119/181 (65%), Gaps = 3/181 (1%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 75
GWA+D++ P +S L + K NLN +SHD+A GLI L+ + +T+V++DTVG E Y
Sbjct: 91 GWALDVLSPNLISTSXLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGXPETY 150
Query: 76 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 135
QA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W F E +++ ++GSG
Sbjct: 151 QARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDYGSG 210
Query: 136 YPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLWESDEMDEDVSSRRSG 194
YP DP+TKAWL H +FGFP VRFSW T + K+ +V+WE E +ED R G
Sbjct: 211 YPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIWEDSEAEED--PERPG 268
Query: 195 K 195
K
Sbjct: 269 K 269
>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|D Chain D, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|G Chain G, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|J Chain J, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|M Chain M, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|P Chain P, Crystal Structure Of Human Rnase H2 Complex
Length = 302
Score = 184 bits (466), Expect = 5e-47, Method: Compositional matrix adjust.
Identities = 87/184 (47%), Positives = 122/184 (66%), Gaps = 6/184 (3%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 75
GWA+D++ P +S ML + K NLN +SHD+A GLI L+ G+ +T+V++DTVG E Y
Sbjct: 93 GWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETY 152
Query: 76 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 135
QA+L Q FP I+ V KAD+LYPVVS ASI AKV RD+ ++ W F E +++ ++GSG
Sbjct: 153 QARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDYGSG 212
Query: 136 YPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLWESDEMDEDVSSRRSG 194
YP DP+TKAWL +H +FGFP VRFSW T + K+ +V+WE + S + G
Sbjct: 213 YPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIWE-----DSASENQEG 267
Query: 195 KRQL 198
R++
Sbjct: 268 LRKI 271
>pdb|3P56|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
pdb|3P56|D Chain D, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 299
Score = 181 bits (459), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 83/166 (50%), Positives = 114/166 (68%), Gaps = 1/166 (0%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 75
GWA+D++ P +S ML + K NLN +SHD+A GLI L+ G+ +T+V++DTVG E Y
Sbjct: 90 GWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETY 149
Query: 76 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 135
QA+L Q FP I+ V KA +LYPVVS ASI AKV RD+ ++ W F E +++ ++GSG
Sbjct: 150 QARLQQSFPGIEVTVKAKAAALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDYGSG 209
Query: 136 YPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLWE 180
YP DP+TKAWL +H +FGFP VRFSW T + K+ +V+WE
Sbjct: 210 YPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIWE 255
>pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
pdb|1EKE|B Chain B, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
Length = 230
Score = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 53/161 (32%), Positives = 82/161 (50%), Gaps = 22/161 (13%)
Query: 22 IDPRELSAKMLNK--NKINLNEISHDS----AIGLITRVLNIGILLTEVYLDTVGD---- 71
++ R L A+ +N+ N INLN+I ++ A LI + LNI E+Y+D
Sbjct: 62 VEKRILEAEEINQLXNSINLNDIEINAFSKVAKNLIEK-LNIRDDEIEIYIDACSTNTKK 120
Query: 72 -----AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAE 126
+K + + +R +IK + KAD+ YPVVS ASI+AK RD + + +
Sbjct: 121 FEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY------K 174
Query: 127 NMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
++ + GSGYP DP+T +L D+ P + R W TC
Sbjct: 175 KIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTC 215
>pdb|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C
Length = 213
Score = 74.7 bits (182), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 44/114 (38%), Positives = 64/114 (56%), Gaps = 8/114 (7%)
Query: 64 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 121
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 122 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIV 175
E + + GSGYP DP T+A+L ++ FP +VR W T +D++
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKITQDMI 209
>pdb|1UAX|A Chain A, Crystal Structure Of The Ribonuclease H2 From Pyrococcus
Horikoshii Ot3
pdb|1UAX|B Chain B, Crystal Structure Of The Ribonuclease H2 From Pyrococcus
Horikoshii Ot3
Length = 220
Score = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 49/170 (28%), Positives = 87/170 (51%), Gaps = 14/170 (8%)
Query: 3 SEAALPKWASNPFGWAVDIIDPREL---SAKMLNKNKINLNEISHDSAIGLITRVLNIGI 59
S+ P F +DI+D + + K +++ ++NE+ + + + ++ I
Sbjct: 41 SKQLTPGQREKLFSKLIDILDDYYVLLVTPKEIDERHHSMNELEAEK---FVVALNSLRI 97
Query: 60 LLTEVYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLR 117
++Y+D+ D +++ + + V+++ KAD+ Y +VS ASI+AKVTRDR +
Sbjct: 98 KPQKIYVDSADVDPKRFASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREI- 156
Query: 118 GWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
E + + FGSGYP DP TK WL ++ FP +VR +W T
Sbjct: 157 -----EKLKQKYGEFGSGYPSDPRTKEWLEEYYKQYGDFPPIVRRTWETA 201
>pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From
Hyperthermophilic Archaeon, Thermococcus Kodakaraensis
Kod1
Length = 213
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 60/106 (56%), Gaps = 8/106 (7%)
Query: 64 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 121
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 122 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
E + + GSGYP DP T+A+L ++ FP +VR W T
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTL 201
>pdb|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C
Length = 221
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 60/106 (56%), Gaps = 8/106 (7%)
Query: 64 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 121
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 122 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
E + + GSGYP DP T+A+L ++ FP +VR W T
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTL 201
>pdb|2DFE|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-200)-C
Length = 209
Score = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 60/106 (56%), Gaps = 8/106 (7%)
Query: 64 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 121
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 122 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
E + + GSGYP DP T+A+L ++ FP +VR W T
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTT 201
>pdb|1X1P|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42)
Length = 212
Score = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 42/106 (39%), Positives = 59/106 (55%), Gaps = 8/106 (7%)
Query: 64 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 121
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 122 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
E + + GSGYP DP T+A+L ++ FP +VR G
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGAGAI 201
>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|E Chain E, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|F Chain F, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus
Length = 217
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 45/153 (29%), Positives = 70/153 (45%), Gaps = 25/153 (16%)
Query: 22 IDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEV-YLDTVGDAEKYQAKLS 80
+ P L +M K +NEI + +I R L E+ Y+D+ + ++
Sbjct: 76 VSPENLDERMAAKT---INEILKECYAEIILR------LKPEIAYVDSPDVIPERLSREL 126
Query: 81 QRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDP 140
+ ++ V KAD YP+V+ ASI+AKV R+R + E + +FGSGY DP
Sbjct: 127 EEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ERLKEKFGDFGSGYASDP 180
Query: 141 ET----KAWLTDHKHIIFGFPSLVRFSWGTCTS 169
T K W+ + PS VR W T ++
Sbjct: 181 RTREVLKEWIASGR-----IPSCVRMRWKTVSN 208
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 45/153 (29%), Positives = 70/153 (45%), Gaps = 25/153 (16%)
Query: 22 IDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEV-YLDTVGDAEKYQAKLS 80
+ P L +M K +NEI + +I R L E+ Y+D+ + ++
Sbjct: 84 VSPENLDERMAAKT---INEILKECYAEIILR------LKPEIAYVDSPDVIPERLSREL 134
Query: 81 QRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDP 140
+ ++ V KAD YP+V+ ASI+AKV R+R + E + +FGSGY DP
Sbjct: 135 EEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ERLKEKFGDFGSGYASDP 188
Query: 141 ET----KAWLTDHKHIIFGFPSLVRFSWGTCTS 169
T K W+ + PS VR W T ++
Sbjct: 189 RTREVLKEWIASGR-----IPSCVRMRWKTVSN 216
>pdb|2X4I|A Chain A, Orf 114a From Sulfolobus Islandicus Rudivirus 1
pdb|2X4I|B Chain B, Orf 114a From Sulfolobus Islandicus Rudivirus 1
pdb|2X4I|C Chain C, Orf 114a From Sulfolobus Islandicus Rudivirus 1
pdb|2X4I|D Chain D, Orf 114a From Sulfolobus Islandicus Rudivirus 1
Length = 114
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 2/85 (2%)
Query: 14 PFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAE 73
P +D ID E + N++ IN I HDS I LI + V + + +
Sbjct: 19 PTKVVIDKIDRLEFCENIDNEDIIN--SIGHDSTIQLINSLCGTTFQKNRVEIKLEKEDK 76
Query: 74 KYQAKLSQRFPSIKFVVSKKADSLY 98
Y ++SQR K + ++ LY
Sbjct: 77 LYVVQISQRLEEGKILTLEEILKLY 101
>pdb|3SNP|A Chain A, Crystal Structure Analysis Of Iron Regulatory Protein 1
In Complex With Ferritin H Ire Rna
pdb|3SNP|B Chain B, Crystal Structure Analysis Of Iron Regulatory Protein 1
In Complex With Ferritin H Ire Rna
pdb|3SN2|A Chain A, Crystal Structure Analysis Of Iron Regulatory Protein 1
In Complex With Transferrin Receptor Ire B Rna
Length = 908
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 12 SNPFGWAVDIIDPRELSAKMLNKNKIN 38
SNPF + + +DP + K N NK++
Sbjct: 21 SNPFAYLAEPLDPAQPGKKFFNLNKLD 47
>pdb|2ZME|B Chain B, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 238
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 26 ELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPS 85
ELS + NK K +I+ D I + +L++GI V +T G +Y +L+++
Sbjct: 45 ELSKSIANKIKDKQGDITEDETIRFKSYLLSMGI-ANPVTRETYGSGTQYHMQLAKQLAG 103
Query: 86 I 86
I
Sbjct: 104 I 104
>pdb|3CUQ|B Chain B, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 218
Score = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 26 ELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPS 85
ELS + NK K +I+ D I + +L++GI V +T G +Y +L+++
Sbjct: 25 ELSKSIANKIKDKQGDITEDETIRFKSYLLSMGI-ANPVTRETYGSGTQYHMQLAKQLAG 83
Query: 86 I 86
I
Sbjct: 84 I 84
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,681,027
Number of Sequences: 62578
Number of extensions: 258669
Number of successful extensions: 638
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 612
Number of HSP's gapped (non-prelim): 20
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)